ParmEd can't infer atomic numbers based on mass or atom names?
On Fri, Dec 9, 2016 at 11:25 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> On Fri, Dec 9, 2016 at 12:18 PM, Brian Radak <brian.radak.accts.gmail.com>
> wrote:
>
> > Oh, you are both right and wrong.
> >
> >
> I talked about atomic_number and HMR, I did not say anything about
> "load_file".
> If you do not provide correct atomic number for your psf, you can't do HMR.
>
>
>
> > >>> parm = parmed.load_file('my.psf')
> >
> > is totally valid, but I had no idea about the (undocumented?) trick of
> >
> >
> there is no trick. The document is in ParmEd's website:
> https://parmed.github.io/ParmEd/html/parmed_api.html
>
> Hai
>
> >>> parmed.tools.actions.XXX(parm, arg_list).execute()
> >
> > Thanks!
> > Brian
> >
> > On Fri, Dec 9, 2016 at 11:07 AM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> >
> > > I don't think ParmED HMR will work with PSF or PDB input (if they don't
> > > have atomi_number information for ParmEd).
> > >
> > > In general, you can access any ParmEd's Action API by
> > >
> > > import parmed as pmd
> > >
> > > parm = pmd.load_file('your.prmtop')
> > > pmd.tools.actions.XXXX(parm, arg_list).execute()
> > > (replace XXXX by something like: HMassRepartition)
> > >
> > > I suggesst to use IPython to explore its (ParmEd) functions.
> > >
> > > Hai
> > >
> > >
> > > On Fri, Dec 9, 2016 at 10:59 AM, Brian Radak <
> > brian.radak.accts.gmail.com>
> > > wrote:
> > >
> > > > Hello,
> > > >
> > > > Is there a simple workflow for using ParmEd to apply hydrogen mass
> > > > repartitioning on PSF/PDB inputs? I gather that this can be done
> > through
> > > > the Python interface, but I can't figure out how to utilize the
> > > > HMassRepartition action in that context.
> > > >
> > > > Thanks,
> > > > Brian
> > > >
> > > > --
> > > > Brian Radak
> > > > Postdoctoral Appointee
> > > > Leadership Computing Facility
> > > > Argonne National Laboratory
> > > >
> > > > 9700 South Cass Avenue, Bldg. 240
> > > > Argonne, IL 60439-4854
> > > > (630) 252-8643
> > > > brian.radak.anl.gov
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> >
> >
> > --
> > Brian Radak
> > Postdoctoral Appointee
> > Leadership Computing Facility
> > Argonne National Laboratory
> >
> > 9700 South Cass Avenue, Bldg. 240
> > Argonne, IL 60439-4854
> > (630) 252-8643
> > brian.radak.anl.gov
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory
9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
brian.radak.anl.gov
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Received on Fri Dec 09 2016 - 09:30:04 PST
